| Caudate nucleus | Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. |
| vaccine | A vaccine is a processed (manufactured) material that has the function to modulate immune responses in a host organism (e.g., human) against a particular target(s) (e.g. a pathogen) in order to prevent or treat disease. |
| vaccination | Vaccination is: an badministering substance in vivob that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response. |
| http://usefulinc.com/ns/doap#Project | |
| http://usefulinc.com/ns/doap#SVNRepository | |
| http://usefulinc.com/ns/doap#Version | |
| portion of tissue | Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. |
| multi-tissue structure | Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. |
| epithelium | Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. |
| peptide | Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. |
| deoxyribonucleic acids | High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. |
| hydrogensulfite | A sulfur oxoanion that has formula HO3S. |
| glucose | |
| 5'-adenylyl sulfate | An acyl sulfate that has formula C10H14N5O10PS. |
| molecular entity | Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. |
| luciferin | A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. |
| sodium chloride | An inorganic chloride salt that has formula ClNa. |
| acrylamide | An acrylamide that has formula C3H5NO. |
| sodium citrate dihydrate | |
| nucleic acid | should be imported from chebi |
| ribonucleic acids | Naturally occurring polyribonucleotides. |
| amino acids | Carboxylic acids containing one or more amino groups. |
| sodium phosphates | |
| ethylenediaminetetraacetic acid | A tetracarboxylic acid that has formula C10H16N2O8. |
| double-stranded DNA | |
| 5-bromo-2-deoxyuridine | |
| chromium-51 | A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. |
| tritiated thymidine | Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.. |
| tris | A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. |
| cell | Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. |
| fibroblast | A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. |
| epithelial cell | A cell that is usually found in a two-dimensional sheet with a free surface. |
| T cell | A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. |
| mast cell | A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. |
| hepatocyte | The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. |
| macrophage | A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. |
| B cell | A lymphocyte of B lineage with the phenotype CD19-positive and surface immunoglobulin-positive. |
| dendritic cell | A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. |
| lymphocyte | A cell of the B cell, T cell, or natural killer cell lineage. |
| CD4-positive, alpha-beta T cell | A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. |
| CD8-positive, alpha-beta T cell | A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. |
| basophil | Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. |
| plasma cell | A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. |
| alpha-beta T cell | A T cell that expresses an alpha-beta T cell receptor complex. |
| CD8-positive, alpha-beta cytotoxic T cell | A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. |
| mature NK T cell | A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. |
| mononuclear cell | A leukocyte with a single non-segmented nucleus in the mature form. |
| soil | Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. |
| podzol | Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. |
| Mouth | |
| Lymph node | |
| Spleen | |
| Body substance | Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Examples: saliva, semen, cerebrospinal fluid, inhaled air, urine, feces, blood, plasma, lymph. |
| Blood | Body substance which consists of plasma and blood cells |
| cytokine production | The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| T cell mediated cytotoxicity | The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. |
| adaptive immune response | An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). |
| cytokine production during immune response | The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels. |
| platelet activating factor production | The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. |
| cytokine production during acute inflammatory response | The synthesis or release of a cytokine following a inflammatory stimulus during an acute inflammatory response, resulting in an increase in its intracellular or extracellular levels. |
| molecular_function | Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. |
| catalytic activity | Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. |
| RNA-directed DNA polymerase activity | Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. |
| cellular_component | The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. |
| glucose metabolic process | The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. |
| immune response | Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. |
| blood coagulation | The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. |
| biological_process | Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. |
| cell proliferation | The multiplication or reproduction of cells, resulting in the expansion of a cell population. |
| gene expression | The process by which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. |
| vascular endothelial growth factor production | The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| B cell receptor complex | An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. |
| connective tissue growth factor production | The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| chemokine production | The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| granulocyte macrophage colony-stimulating factor production | The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| hepatocyte growth factor production | The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| type I interferon production | The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. |
| interferon-gamma production | The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. |
| interleukin-1 beta production | The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-1 production | The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-10 production | The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-11 production | The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-12 production | The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-13 production | The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-14 production | The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-15 production | The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-16 production | The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-17 production | The appearance of interleukin-17 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-18 production | The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-19 production | The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-2 production | The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-20 production | The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-21 production | The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-22 production | The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-23 production | The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-24 production | The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-25 production | The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-26 production | The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-27 production | The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-3 production | The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-4 production | The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-5 production | The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-6 production | The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-7 production | The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-8 production | The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| interleukin-9 production | The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| TRAIL production | The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| tumor necrosis factor production | The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| lymphotoxin A production | The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| transforming growth factor-beta1 production | The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| transforming growth factor-beta2 production | The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| transforming growth factor-beta3 production | The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. |
| DNA polymerase activity | Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer. |
| type III interferon production | The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type III interferons are members of the interferon-lambda gene family. |
| T cell proliferation | The expansion of a T cell population by cell division. Follows T cell activation. |
| T cell receptor complex | A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. |
| immunoglobulin complex, circulating | An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. |
| DNA polymerase complex | A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. |
| MHC protein complex | A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. |
| membrane-bounded organelle | Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. |
| protein complex | Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups. |
| response to stimulus | A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. |
| Insulin resistance | |
| IAO:0000001 | |
| IAO:0000003 | |
| IAO:0000005 | |
| IAO:0000006 | |
| IAO:0000010 | |
| IAO:0000027 | |
| IAO:0000030 | |
| IAO:0000032 | |
| IAO:0000033 | |
| IAO:0000037 | |
| IAO:0000038 | |
| IAO:0000055 | |
| IAO:0000078 | |
| IAO:0000088 | |
| IAO:0000098 | |
| IAO:0000100 | |
| IAO:0000101 | |
| IAO:0000104 | |
| IAO:0000109 | |
| IAO:0000178 | |
| IAO:0000179 | |
| IAO:0000183 | |
| IAO:0000184 | |
| IAO:0000186 | |
| IAO:0000306 | |
| Cricetinae | |
| Phodopus | |
| Phodopus sungorus | |
| Muridae | |
| Mus | |
| Mus musculus | |
| Rattus | |
| Rattus norvegicus | |
| Viruses | |
| Asteroideae | |
| Heliantheae | |
| Mutisieae | |
| Obtectomera | |
| Rhodobacter | |
| canis group | |
| phagocytophilum group | |
| Rhodobacter sphaeroides | |
| mitosporic Filobasidiales | |
| Thlaspi caerulescens | |
| Cryptococcus [NCBITaxon:107441] | |
| Rhodospirillum | |
| Rhodospirillum rubrum | |
| Chloroflexaceae | |
| Nectriaceae | |
| Chloroflexus | |
| Chloroflexus aurantiacus | |
| Coronaviridae | |
| Coronavirus | |
| Penaeoidea | |
| pseudomallei group | |
| Cyanobacteria | |
| Chroococcales | |
| Synechococcus | |
| Polytrichopsida | |
| Populus tremula | |
| Synechocystis | |
| spotted fever group | |
| typhus group | |
| Synechocystis sp. | |
| Saccharomyces kudriavzevii | |
| Saccharomyces mikatae | |
| Funariidae | |
| Synechocystis sp. PCC 6803 | |
| Oscillatoriales | |
| Nostocales | |
| Nostocaceae | |
| Anabaena | |
| Anabaena variabilis | |
| Teleostomi | |
| Euteleostomi | |
| Nostoc | |
| Sphingobacteria | |
| mitosporic Saccharomycetales | |
| Populus tomentosa | |
| Brucellaceae | |
| Sulfolobaceae | |
| Deinococcales | |
| Coxiellaceae | |
| Legionellales | |
| Burkholderiaceae | |
| unclassified Burkholderiales | |
| Thermoanaerobacter tengcongensis | |
| Chromadorea | |
| Bombyciformes | |
| Acidithiobacillus | |
| Trichodesmium | |
| Trichodesmium erythraeum | |
| Paracoccidioides brasiliensis | |
| Proteobacteria | |
| Neoteleostei | |
| Eurypterygii | |
| Ctenosquamata | |
| Acanthomorpha | |
| Euacanthomorpha | |
| Holacanthopterygii | |
| Gammaproteobacteria | |
| Firmicutes | |
| Leuconostoc | |
| Leuconostoc mesenteroides | |
| Oenococcus oeni | |
| Pediococcus | |
| Pediococcus pentosaceus | |
| Staphylococcus | |
| Staphylococcus aureus | |
| Polytrichum juniperinum | |
| Deinococcus-Thermus | |
| Deinococcus | |
| Deinococcus radiodurans | |
| Euacanthopterygii | |
| Streptococcaceae | |
| Streptococcus | |
| Streptococcus gordonii | |
| Streptococcus suis | |
| Streptococcus mutans | |
| Streptococcus agalactiae | |
| Streptophytina | |
| Streptococcus pneumoniae | |
| Magnetospirillum | |
| Streptococcus pyogenes | |
| Thlaspi | |
| Burkholderia mallei | |
| Penaeus | |
| Coffea | |
| Coffea arabica | |
| Burkholderia fungorum | |
| Enterococcus | |
| Enterococcus faecalis | |
| Enterococcus faecium | |
| Gerbera | |
| Xanthomonadales | |
| Pseudomonadaceae | |
| Alteromonadales | |
| Vibrionales | |
| Pasteurellales | |
| Lactococcus | |
| Lactococcus lactis | |
| Spirochaetales | |
| Pseudomonas aeruginosa group | |
| Pseudomonas fluorescens group | |
| Pseudomonas putida group | |
| Spirochaetaceae | |
| Borrelia | |
| Pteridaceae | |
| Bacillales | |
| Bacillus | |
| Borrelia burgdorferi | |
| Bacillus anthracis | |
| Pinus [NCBITaxon:139271] | |
| Bacillus cereus | |
| Bacillus subtilis | |
| Mycetozoa | |
| Methanothermobacter | |
| Methanothermobacter thermautotrophicus | |
| Ehrhartoideae | |
| Pooideae | |
| Panicoideae | |
| PACCAD clade | |
| Oryzeae | |
| Poeae | |
| Triticeae | |
| Andropogoneae | |
| Saccharomycotina | |
| Pezizomycotina | |
| Dothideomycetes et Chaetothyriomycetes incertae sedis | |
| Eurotiomycetes | |
| Sordariomycetes | |
| Sordariomycetes incertae sedis | |
| Schizosaccharomycetes | |
| Magnaporthe | |
| Magnaporthe grisea | |
| Clostridium | |
| Clostridium acetobutylicum | |
| Clostridium botulinum | |
| Clostridium sporogenes | |
| Clostridium thermocellum | |
| Moorella thermoacetica | |
| Tremellomycetidae | |
| Homobasidiomycetes | |
| Caulobacter vibrioides | |
| Plantaginaceae | |
| Group 2 species | |
| Treponema | |
| Lactobacillus | |
| Treponema denticola | |
| Citrus aurantiifolia | |
| Lactobacillus gasseri | |
| Lactobacillus sakei | |
| Treponema pallidum | |
| Lactobacillus salivarius | |
| Listeria | |
| Phaseoleae | |
| Trifolieae | |
| Vicieae | |
| Loteae | |
| Listeria monocytogenes | |
| Listeria innocua | |
| Corynebacteriaceae | |
| Actinomyces | |
| Actinomyces naeslundii | |
| Novosphingobium | |
| Heterobasidiomycetes | |
| Bifidobacterium | |
| Ixoroideae | |
| Coffeeae | |
| Corynebacterium | |
| Rosoideae | |
| Corynebacterium glutamicum | |
| Passeroidea | |
| Thermoanaerobacter | |
| Actinobacteria (class) | |
| Mycobacteriaceae | |
| Mycobacterium | |
| Mycobacterium leprae | |
| Mycobacterium tuberculosis | |
| Gerbera hybrid cultivar | |
| Deinococcaceae | |
| Enterogona | |
| Thermoprotei | |
| Methanobacteria | |
| Halobacteria | |
| Thermoplasmata | |
| Thermococci | |
| Archaeoglobi | |
| Psathyrellaceae | |
| Coprinopsis | |
| Drosophiliti | |
| Entomoplasmatales | |
| Actinopteri | |
| Elopocephala | |
| Clupeocephala | |
| Otophysi | |
| Cypriniphysi | |
| Otocephala | |
| Clostridia | |
| Clostridiales | |
| Peptococcaceae | |
| Thermoanaerobacteriaceae | |
| Bacillaceae | |
| Listeriaceae | |
| Alicyclobacillaceae | |
| Lactobacillales | |
| Neognathi | |
| Salmonoidei | |
| Anurophorinae | |
| Cryptopygus | |
| Cryptopygus antarcticus | |
| Aquificae (class) | |
| Magnetospirillum magnetotacticum | |
| Streptomyces | |
| Thermotogae (class) | |
| Thermotogaceae | |
| Deinococci | |
| Orbiliomycetes | |
| Orbiliales | |
| Zinnia | |
| Streptomyces coelicolor | |
| Lepidium | |
| Campylobacter | |
| Desulfovibrionaceae | |
| Pleuronichthys | |
| Pleuronichthys verticalis | |
| Corynebacterium glutamicum ATCC 13032 | |
| Campylobacter jejuni | |
| Pancrustacea | |
| Mandibulata | |
| Bacteria | |
| Sphingobacteriales | |
| Aquificae | |
| Chloroflexi | |
| Thermotogae | |
| Actinobacteria | |
| Thermobifida fusca | |
| Fusobacteria (class) | |
| Fusobacterales | |
| Fusobacteriaceae | |
| Spirochaetes | |
| Spirochaetes (class) | |
| Actinomycetales | |
| Chlamydiae | |
| Chlamydiae (class) | |
| Rhodospirillales | |
| Rhodobacterales | |
| Sphingomonadales | |
| Caulobacterales | |
| Herminiimonas arsenicoxydans | |
| Actinomycetaceae | |
| Streptomycetaceae | |
| Methylophilales | |
| Neisseriales | |
| Rhodocyclales | |
| Homo/Pan/Gorilla group | |
| Mycoplasmatales | |
| Pasteuria nishizawae | |
| Helicobacter | |
| Mycoplasmataceae | |
| Mycoplasma | |
| Mycoplasma genitalium | |
| Helicobacter pylori | |
| Streptococcus mutans UA159 | |
| Mycoplasma pneumoniae | |
| Mycoplasma pulmonis | |
| Ureaplasma | |
| Ureaplasma urealyticum | |
| Desulfovibrionales | |
| Geobacteraceae | |
| Campylobacterales | |
| Mesoplasma florum | |
| Archaea | |
| Methanobacteriales | |
| Methanobacteriaceae | |
| Sylvia communis | |
| Lymnaeoidea | |
| Antirrhineae | |
| Bifidobacterium longum | |
| Mutisioideae | |
| Methanosarcinaceae | |
| Methanosarcina | |
| Methanosarcina barkeri | |
| Methanosarcina mazei | |
| Methanococcoides | |
| Hypocreomycetidae | |
| Sordariomycetidae | |
| Archaeoglobales | |
| Archaeoglobaceae | |
| Archaeoglobus | |
| Archaeoglobus fulgidus | |
| Halobacteriales | |
| Halobacteriaceae | |
| Halobacterium | |
| Halobacterium salinarum | |
| Halobacterium sp. | |
| Burkholderiales Genera incertae sedis | |
| Haloferax volcanii | |
| Methanomicrobia | |
| Acidithiobacillales | |
| Acidithiobacillaceae | |
| Haloferax | |
| Thermococcales | |
| Thermococcaceae | |
| Pyrococcus | |
| Thermoproteales | |
| Thermoproteaceae | |
| Thermoproteus | |
| Thermoproteus tenax | |
| Rhizobium/Agrobacterium group | |
| Sinorhizobium/Ensifer group | |
| Paxilineae | |
| SARS coronavirus | |
| Sulfolobales | |
| Sulfolobus | |
| Sulfolobus acidocaldarius | |
| Sulfolobus solfataricus | |
| Thermoplasmatales | |
| Thermoplasma | |
| Thermoplasma acidophilum | |
| Rubus | |
| magnoliids | |
| Thermotoga | |
| Thermotoga maritima | |
| Brucella | |
| Brucella abortus | |
| Rutaceae | |
| Xylella | |
| Xylella fastidiosa | |
| Saliceae | |
| Moniliformopses | |
| Thermotogales | |
| Rubiaceae | |
| Rubrobacterineae | |
| Dechloromonas aromatica | |
| Francisella | |
| Xenopus [NCBITaxon:262014] | |
| Francisella tularensis | |
| Crocosphaera | |
| Crocosphaera watsonii | |
| Francisella tularensis subsp. novicida | |
| Rickettsia sibirica subgroup | |
| Citrus | |
| Citrus sinensis | |
| Aquifex | |
| Nostoc punctiforme | |
| Saccharomyces paradoxus | |
| Saccharomyces pastorianus | |
| Eukaryota | |
| Bovinae | |
| Coregonus | |
| Rubrivivax | |
| Rubrivivax gelatinosus | |
| Ralstonia syzygii | |
| Sinorhizobium | |
| Alphaproteobacteria | |
| Betaproteobacteria | |
| Deltaproteobacteria | |
| Geobacter | |
| Geobacter metallireducens | |
| Staphylococcus aureus subsp. aureus MSSA476 | |
| Burkholderia pseudomallei | |
| Trichocomaceae | |
| Pseudomonas | |
| Pseudomonas aeruginosa | |
| Phaeophyceae | |
| Ectocarpales | |
| Ectocarpaceae | |
| Ectocarpus | |
| Ectocarpus siliculosus | |
| Crenarchaeota | |
| Euryarchaeota | |
| Salmonella enterica | |
| Burkholderia cepacia | |
| Cryptococcus gattii | |
| Methanococcoides burtonii | |
| Pseudomonas fluorescens | |
| Veillonella | |
| Veillonella parvula | |
| Epsilonproteobacteria | |
| Ceratopteris | |
| Ceratopteris thalictroides | |
| Vitis vinifera | |
| Hypocrea | |
| Collembola | |
| Lachancea | |
| Pseudomonas putida | |
| Mesobatrachia | |
| Pipoidea | |
| Herminiimonas | |
| Chlorophyta | |
| Chlamydomonadales | |
| Ralstonia solanacearum | |
| Chlamydomonadaceae | |
| Chlamydomonas | |
| Chlamydomonas reinhardtii | |
| Cyprinoidea | |
| Pleuronectoidei | |
| Tetraodontiformes | |
| Tetraodontoidei | |
| Tetraodontidae | |
| Takifugu | |
| Takifugu rubripes | |
| Schistosomatoidea | |
| Schistosomatidae | |
| Laurasiatheria | |
| Euarchontoglires | |
| Glires | |
| Simiiformes | |
| Cercopithecoidea | |
| Hominoidea | |
| Chlorophyceae | |
| Saccharophagus | |
| Embryophyta | |
| Bifidobacteriaceae | |
| Mollicutes | |
| Acidaminococcaceae | |
| Clostridiaceae | |
| Rhodobacteraceae | |
| Burkholderia | |
| Methylophilaceae | |
| Thiomonas | |
| Xanthomonadaceae | |
| Synechococcus elongatus | |
| Chloroflexi (class) | |
| Chloroflexales | |
| Fusobacteria | |
| Aquificales | |
| Bryophyta | |
| Polytrichales | |
| Polytrichaceae | |
| Polytrichum | |
| Bryopsida | |
| Funariales | |
| Funariaceae | |
| Physcomitrella | |
| Physcomitrella patens | |
| Buchnera | |
| Rubus idaeus | |
| Sophophora | |
| melanogaster group | |
| melanogaster subgroup | |
| obscura group | |
| pseudoobscura subgroup | |
| Lycopodiophyta | |
| Isoetopsida | |
| Selaginellales | |
| Teleostei | |
| Euteleostei | |
| Selaginellaceae | |
| Acanthopterygii | |
| Selaginella | |
| Percomorpha | |
| Tetradontoidea | |
| Paracanthopterygii | |
| Ostariophysi | |
| Tetrapoda | |
| Amniota | |
| Theria | |
| Sauria | |
| Filicophyta | |
| Filicales | |
| Ralstonia pickettii | |
| Filicopsida | |
| Bartonella grahamii | |
| Dictyosteliida | |
| Viridiplantae | |
| Coniferophyta | |
| Lepidium sativum | |
| Coniferales | |
| Fungi/Metazoa group | |
| Eremothecium gossypii | |
| Eremothecium | |
| Aspergillus terreus | |
| Pinaceae | |
| Onygenales | |
| Metazoa | |
| Bilateria | |
| Acoelomata | |
| Pseudocoelomata | |
| Picea | |
| Tylenchina | |
| Tylenchoidea | |
| Heteroderinae | |
| Picea glauca | |
| Coelomata | |
| Protostomia | |
| Neoptera | |
| Pinus | |
| Endopterygota | |
| Pinus radiata | |
| Deuterostomia | |
| Sciurognathi | |
| Carnivora | |
| Alveolata | |
| stramenopiles | |
| Euglenozoa | |
| Cricetidae | |
| Muroidea | |
| Xanthomonas | |
| Felinae | |
| Xanthomonas campestris | |
| Streptomyces avermitilis | |
| Entomoplasmataceae | |
| Lactobacillaceae | |
| Magnoliophyta | |
| Rickettsieae | |
| Xanthomonas campestris pv. campestris | |
| Magnoliales | |
| Magnoliaceae | |
| Francisellaceae | |
| Liriodendron | |
| Liriodendron tulipifera | |
| Zinnia elegans | |
| Lotus japonicus | |
| Schizosaccharomycetales | |
| mitosporic Trichocomaceae | |
| mitosporic Onygenales | |
| Strongyloides ratti | |
| Heterodera | |
| Apoidea | |
| Cannabaceae | |
| Cannabis | |
| Cannabis sativa | |
| Fagales | |
| Betula | |
| Betula pendula | |
| Cryptosporidiidae | |
| Azotobacter group | |
| Betulaceae | |
| Azotobacter | |
| ssRNA positive-strand viruses, no DNA stage | |
| Azotobacter vinelandii | |
| Streptophyta | |
| Suina | |
| Pecora | |
| Equus subg. Equus | |
| Rhizobiales | |
| Agrobacterium | |
| Rickettsia sibirica | |
| Agrobacterium tumefaciens | |
| BEP clade | |
| Vitaceae | |
| Vitis | |
| Isotomidae | |
| Sylviidae | |
| Malpighiales | |
| Neosartorya | |
| Neosartorya fischeri | |
| Desulfitobacterium | |
| Salicaceae | |
| Populus | |
| Populus trichocarpa | |
| Populus trichocarpa x Populus deltoides | |
| Populus deltoides | |
| Brassicales | |
| Brassicaceae | |
| Arabidopsis | |
| Arabidopsis thaliana | |
| Brassica | |
| Brassica juncea | |
| Brassica napus | |
| Brassica rapa | |
| Rosales | |
| Rosaceae | |
| Aedes/Ochlerotatus group | |
| Ditrysia | |
| Bombycoidea | |
| Noctuoidea | |
| Estrildidae | |
| Viannia | |
| Leishmania braziliensis species complex | |
| Haplorrhini | |
| Rhizobium | |
| Feliformia | |
| Caniformia | |
| Fabaceae | |
| Mesorhizobium loti | |
| Papilionoideae | |
| Sinorhizobium meliloti | |
| Bartonella henselae | |
| Rhizobium leguminosarum | |
| Glycine | |
| Glycine max | |
| Leishmania [NCBITaxon:38568] | |
| Leishmania infantum species complex | |
| Leishmania donovani species complex | |
| Leishmania major species complex | |
| Leishmania mexicana species complex | |
| Diprotodontia | |
| Lotus | |
| Medicago | |
| Medicago sativa | |
| Medicago truncatula | |
| Poales | |
| Pisum | |
| Pisum sativum | |
| Paracoccidioides | |
| Trifolium | |
| Trifolium repens | |
| Murinae | |
| Cyprininae | |
| Rasborinae | |
| Trypanozoon | |
| Oryza sativa (indica cultivar-group) | |
| Oryza sativa (japonica cultivar-group) | |
| Linaceae | |
| Linum | |
| Linum usitatissimum | |
| Thraupini | |
| Estrildinae | |
| Vitales | |
| Methylobacillus | |
| Moss Superclass V | |
| Methylobacillus flagellatus | |
| Gentianales | |
| Mammalia | |
| Solanales | |
| Solanaceae | |
| Capsicum | |
| Capsicum annuum | |
| Solanum lycopersicum | |
| Nicotiana | |
| Nicotiana benthamiana | |
| Neosartorya fennelliae | |
| Solanum | |
| Solanum tuberosum | |
| Glossata | |
| Neolepidoptera | |
| Heteroneura | |
| Mycosphaerella | |
| Rhodospirillaceae | |
| Sphingomonadaceae | |
| Lamiales | |
| Antirrhinum | |
| Antirrhinum majus | |
| Neopterygii | |
| Batrachia | |
| Protacanthopterygii | |
| Plasmodium (Vinckeia) | |
| Plasmodium (Laverania) | |
| Culicoidea | |
| Sapindales | |
| Asterales | |
| Asteraceae | |
| Rubrobacter | |
| Aconoidasida | |
| Eimeriorina | |
| Candida dubliniensis | |
| Solanoideae | |
| Nicotianoideae | |
| Nicotianeae | |
| Capsiceae | |
| Solaneae | |
| Thiomonas sp. 3As | |
| Moorella group | |
| Trichoderma reesei QM6a | |
| Sylvia | |
| Dinosauria | |
| Saurischia | |
| Theropoda | |
| Coelurosauria | |
| Muscomorpha | |
| Schizophora | |
| Acalyptratae | |
| Ephydroidea | |
| Culicimorpha | |
| Anophelinae | |
| Culicinae | |
| Drosophilinae | |
| Cyanothece | |
| Cyanothece sp. ATCC 51142 | |
| Moorella | |
| Liliopsida | |
| Cellia | |
| Pyretophorus | |
| gambiae species complex | |
| Dictyostelium discoideum | |
| Poaceae | |
| Hordeum | |
| Hordeum vulgare | |
| Lolium | |
| Lolium perenne | |
| Oryza | |
| Oryza sativa | |
| Triticum | |
| Triticum aestivum | |
| Triticum turgidum subsp. durum | |
| Triticum turgidum | |
| Zea | |
| Zea mays | |
| Festuca | |
| Festuca arundinacea | |
| Staphylococcus aureus subsp. aureus | |
| Mesoplasma | |
| Oenococcus | |
| Thermoplasmataceae | |
| Moraxellaceae | |
| Drosophilini | |
| Drosophilina | |
| Acinetobacter | |
| Acinetobacter baumannii | |
| Orbiliaceae | |
| Tetraodon | |
| commelinids | |
| Fungi | |
| Schizotrypanum | |
| Agrotis | |
| Agrotis segetum | |
| Neisseriaceae | |
| Neisseria | |
| Neisseria gonorrhoeae | |
| Neisseria meningitidis | |
| Ralstonia | |
| Geospiza | |
| Geospiza conirostris | |
| Geospiza fortis | |
| Geospiza magnirostris | |
| Geospiza scandens | |
| Ascomycota | |
| Saccharomycetes | |
| Saccharomycetales | |
| Saccharomycetaceae | |
| Novosphingobium aromaticivorans | |
| Schizosaccharomycetaceae | |
| Schizosaccharomyces | |
| Schizosaccharomyces pombe | |
| Kluyveromyces | |
| Kluyveromyces waltii | |
| Pichia | |
| Pichia pastoris | |
| Lycopersicon | |
| Saccharomyces | |
| Saccharomyces bayanus | |
| Rubrobacter xylanophilus | |
| Saccharomyces cerevisiae | |
| Desulfitobacterium hafniense | |
| Lachancea kluyveri | |
| Thermoplasma volcanium | |
| Eurotiales | |
| Aspergillus | |
| Insecta | |
| Aspergillus clavatus | |
| Alcaligenaceae | |
| Aspergillus niger | |
| Aspergillus fumigatus | |
| Heterodera glycines | |
| Hypocreales | |
| Gibberella | |
| Hypocreaceae | |
| Chlamydiae/Verrucomicrobia group | |
| Chlamydiales | |
| Sordariales | |
| Neurospora | |
| Neurospora crassa | |
| Hypocrea jecorina | |
| Sordaria | |
| Sordaria macrospora | |
| Sordariaceae | |
| Ciona savignyi | |
| Bordetella | |
| Bordetella bronchiseptica | |
| Bordetella pertussis | |
| Basidiomycota | |
| Festuca rubra | |
| Ustilaginomycetes | |
| Ustilaginales | |
| Ustilaginaceae | |
| Ustilago | |
| Ustilago maydis | |
| Leymus | |
| Hymenomycetes | |
| Aphyllophorales | |
| Corticiaceae | |
| Phanerochaete | |
| Phanerochaete chrysosporium | |
| Agaricales | |
| Xanthomonas axonopodis | |
| Coprinopsis cinerea | |
| Stegomyia | |
| Culicini | |
| Paxillaceae | |
| Paxillus | |
| Pyrococcus horikoshii | |
| mitosporic Orbiliaceae | |
| Monacrosporium | |
| Zymomonas | |
| Zymomonas mobilis | |
| Enterobacteriaceae | |
| Mycosphaerella graminicola | |
| Candida | |
| Candida albicans | |
| Candida glabrata | |
| Pinus resinosa | |
| Gibberella zeae | |
| Panagrolaimoidea | |
| Rhabditoidea | |
| Peloderinae | |
| Escherichia | |
| Escherichia coli | |
| Agrotis ipsilon | |
| Kinetoplastida | |
| Trypanosomatidae | |
| Leishmania | |
| Leishmania braziliensis | |
| Leishmania donovani | |
| Leishmania major | |
| Leishmania mexicana | |
| Leishmania infantum | |
| Trypanosoma | |
| Trypanosoma brucei | |
| Trypanosoma cruzi | |
| Dictyostelium | |
| Apicomplexa | |
| Coccidia | |
| Burkholderia thailandensis | |
| Coniferopsida | |
| Tracheophyta | |
| Spermatophyta | |
| Cryptosporidium | |
| Cryptosporidium parvum | |
| Haemosporida | |
| Plasmodium | |
| Plasmodium berghei | |
| Plasmodium falciparum | |
| Salmonella | |
| Salmonella enteritidis | |
| Taeniopygia | |
| Taeniopygia guttata | |
| Coregonus clupeaformis | |
| Salmonella typhi | |
| Salmonella typhimurium | |
| Eumetazoa | |
| Neosartorya fischeri group | |
| Platyhelminthes | |
| Trematoda | |
| Digenea | |
| Strigeidida | |
| Schistosoma | |
| Schistosoma japonicum | |
| Schistosoma mansoni | |
| Emberizinae | |
| Nematoda | |
| Rhabditida | |
| Caenorhabditis | |
| Caenorhabditis briggsae | |
| Caenorhabditis elegans | |
| Rhabditidae | |
| Strongyloididae | |
| Strongyloides | |
| Spirurida | |
| Brugia | |
| Brugia malayi | |
| Yersinia | |
| Ustilaginomycetidae | |
| Filarioidea | |
| Onchocercidae | |
| Tylenchida | |
| Heteroderidae | |
| Yersinia pestis | |
| Aquifex aeolicus | |
| Vibrionaceae | |
| Mollusca | |
| Gastropoda | |
| Buchnera sp. | |
| Borrelia burgdorferi group | |
| Aquificaceae | |
| Pulmonata | |
| Basommatophora | |
| Planorbidae | |
| Biomphalaria | |
| Biomphalaria glabrata | |
| Photobacterium | |
| Vibrio | |
| Arthropoda | |
| Crustacea | |
| Vibrio cholerae | |
| Malacostraca | |
| Eucarida | |
| Decapoda | |
| Dendrobranchiata | |
| Penaeidae | |
| Penaeus monodon | |
| Mesorhizobium | |
| Thermoanaerobacteriales | |
| Bacteroidetes/Chlorobi group | |
| delta/epsilon subdivisions | |
| Boletales | |
| Phyllobacteriaceae | |
| Desulfuromonadales | |
| Hexapoda | |
| Lepidoptera | |
| Bombycidae | |
| Bombyx | |
| Bombyx mori | |
| Apinae | |
| Noctuidae | |
| Paxillus involutus | |
| Pasteurellaceae | |
| eudicotyledons | |
| asterids | |
| rosids | |
| Actinobacillus | |
| Diptera | |
| Nematocera | |
| Actinobacillus pleuropneumoniae | |
| Culicidae | |
| Aedes | |
| Aedes aegypti | |
| Anopheles | |
| Anopheles gambiae | |
| Fabales | |
| Brachycera | |
| Eumalacostraca | |
| Drosophilidae | |
| Drosophila | |
| Drosophila erecta | |
| Drosophila mauritiana | |
| Drosophila melanogaster | |
| Thiotrichales | |
| Pseudomonadales | |
| Alteromonadaceae | |
| Helicobacteraceae | |
| Campylobacteraceae | |
| Drosophila orena | |
| Drosophila pseudoobscura | |
| Drosophila sechellia | |
| Haemophilus | |
| Drosophila simulans | |
| Drosophila teissieri | |
| Drosophila yakuba | |
| Haemophilus influenzae | |
| Dechloromonas | |
| Hymenoptera | |
| Apocrita | |
| Photobacterium profundum | |
| Aculeata | |
| Monacrosporium haptotylum | |
| Pasteurella | |
| Apidae | |
| Apis | |
| Apis mellifera | |
| Pasteurella multocida | |
| Pterygota | |
| Ferroplasma | |
| Caulobacter | |
| Oxalobacteraceae | |
| Populus euphratica | |
| Eucoccidiorida | |
| Rhodocyclaceae | |
| Rickettsiales | |
| Anaplasma | |
| Nidovirales | |
| Caulobacteraceae | |
| Chordata | |
| Urochordata | |
| Ascidiacea | |
| Phlebobranchia | |
| Cionidae | |
| Ciona | |
| Ciona intestinalis | |
| Bartonellaceae | |
| Stolidobranchia | |
| Pyuridae | |
| Bartonella | |
| Herdmania | |
| Herdmania momus | |
| Vertebrata | |
| Rickettsiaceae | |
| Coxiella | |
| Mycobacterium tuberculosis complex | |
| Coxiella burnetii | |
| Gnathostomata | |
| Rickettsia | |
| Rickettsia conorii | |
| Rickettsia prowazekii | |
| Rickettsia rickettsii | |
| Euphyllophyta | |
| Actinopterygii | |
| Cypriniformes | |
| Cyprinidae | |
| Danio | |
| Danio rerio | |
| Cyprinus | |
| Cyprinus carpio | |
| Arthropleona | |
| Entomobryoidea | |
| Ellipura | |
| Salmoniformes | |
| Salmonidae | |
| Oncorhynchus | |
| Oncorhynchus mykiss | |
| Salmo | |
| Bartonella quintana | |
| Salmo salar | |
| Salmo trutta | |
| Gadiformes | |
| Gadidae | |
| Gadus | |
| Gadus morhua | |
| Burkholderiales | |
| Populus tremula x Populus alba | |
| Chlamydiaceae | |
| Chlamydia | |
| Magnaporthaceae | |
| Perciformes | |
| Percoidei | |
| Chlamydia trachomatis | |
| Sparidae | |
| Sparus | |
| Sparus aurata | |
| Leuconostocaceae | |
| Enterococcaceae | |
| Rhizobiaceae | |
| Pleuronectiformes | |
| Pleuronectidae | |
| Platichthys | |
| Platichthys flesus | |
| Sarcopterygii | |
| Amphibia | |
| Apini | |
| Anura | |
| Pipidae | |
| Xenopus | |
| Xenopus laevis | |
| Chlamydophila | |
| Chlamydophila pneumoniae | |
| Xenopodinae | |
| Silurana | |
| Xenopus tropicalis | |
| Nocardiopsaceae | |
| Thermobifida | |
| Sauropsida | |
| Fusobacterium | |
| Archosauria | |
| Rubrobacteridae | |
| Rubrobacterales | |
| Rubrobacteraceae | |
| Actinobacteridae | |
| Bifidobacteriales | |
| Actinomycineae | |
| Corynebacterineae | |
| Streptomycineae | |
| Streptosporangineae | |
| Fusobacterium nucleatum | |
| Dicondylia | |
| Amphiesmenoptera | |
| Citrus clementina | |
| Triticum turgidum subsp. dicoccoides | |
| Paxillus filamentosus | |
| Pasteuria | |
| Leymus cinereus | |
| Leymus triticoides | |
| Saccharophagus degradans | |
| Bacillus cereus group | |
| Bacillus halodurans | |
| Geospiza difficilis | |
| Desulfovibrio | |
| Desulfovibrio desulfuricans | |
| Aves | |
| Burkholderia cepacia complex | |
| Neognathae | |
| Panarthropoda | |
| Flexibacteraceae | |
| Craniata | |
| Galliformes | |
| Phasianidae | |
| Ferroplasmaceae | |
| Gallus | |
| Gallus gallus | |
| Phasianinae | |
| Filobasidiales | |
| Staphylococcaceae | |
| Bacilli | |
| Passeriformes | |
| Fringillidae | |
| Enterobacteriales | |
| Cetartiodactyla | |
| core eudicotyledons | |
| eurosids I | |
| eurosids II | |
| campanulids | |
| lamiids | |
| Acidithiobacillus ferrooxidans | |
| Bartonella koehlerae | |
| Metatheria | |
| Xanthomonas axonopodis pv. citri | |
| Macropodidae | |
| Macropus | |
| Mycosphaerellaceae | |
| Macropus eugenii | |
| Eutheria | |
| Anaplasmataceae | |
| Ehrlichia | |
| Ehrlichia canis | |
| Primates | |
| Methanosarcinales | |
| Platyrrhini | |
| Anaplasma phagocytophilum | |
| Callitrichinae | |
| Callithrix | |
| Callithrix jacchus | |
| Cebidae | |
| Noctuinae | |
| Catarrhini | |
| Cercopithecidae | |
| Cercopithecinae | |
| Macaca | |
| Macaca fascicularis | |
| Macaca fuscata | |
| Macaca mulatta | |
| Pan | |
| Pan troglodytes | |
| Pongo | |
| Pongo pygmaeus | |
| Hominidae | |
| Homo | |
| Homo sapiens | |
| Canidae | |
| Canis | |
| Canis familiaris | |
| Vulpes | |
| Vulpes vulpes | |
| Felidae | |
| Felis | |
| Felis catus | |
| Ferroplasma acidarmanus | |
| Bacteroidetes | |
| Cytophaga | |
| Perissodactyla | |
| Equidae | |
| Equus | |
| Equus caballus | |
| Suidae | |
| Sus | |
| Sus scrofa | |
| Ruminantia | |
| Cytophaga hutchinsonii | |
| Festuca brevipila | |
| Festuca rubra subsp. fallax | |
| Festuca rubra subsp. littoralis | |
| Bovidae | |
| Bos | |
| Bos taurus | |
| Bos indicus | |
| Ovis | |
| Ovis aries | |
| Caprinae | |
| Tetraodon nigroviridis | |
| Rodentia | |
| role of being consumer safety officer | the role of a human being that is realized by enforcing regulations to ensure consumer safety |
| fluorescent reporter intensity | The fluorescent reporter intensity is a datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. |
| planned process | A processual entity that realizes a plan which is the concretization of a plan specification. |
| regulator role | Regulator role is a regulatory role involved with making and/or enforcing relevant legislation and governmental orders |
| biological feature identification objective | Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. |
| regulation-assigned role | Regulation-assigned role is a regulatory role defined by legislation or governmental orders |
| regulatory role | Regulatory role is a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. |
| supplier role | Supplier is a worker who provides reagents, subjects and other materials used in a study; this role generally occurs before the study, but could occur during the study |
| contract research organization role | Contract research organization is a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution |
| list-mode data file | A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. |
| classified data set | A classified data set is a data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. |
| reference substance role | a role inhering in a substance that is realized when characteristics or responses elicited by the substance are used for comparison or reference. |
| cytological stain role | is a role of a stain that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization |
| centrifuge pellet role | pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. |
| clinical research coordinator role | A clinical research coordinator is a worker role comprised of handling the administrative duties of a trial or study. |
| supernatant role | supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. |
| chromatography column | Column chromatography in chemistry is a tube (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. |
| drug role | Drug role is a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism |
| pump valve switch | A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. |
| xenotransplantation | is the transplantation of living cells, tissues or norgans from one species to another such as from pigs to humans |
| physical document | A physical document is an object serving as a record of information by means of symbolic marks. |
| waiting | not actively doing anything to a material for a duration of time. |
| processed material | Is a material entity that is created or changed during material processing. |
| chromatography device | A Chromatography device is a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. |
| mass spectrometer | A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum |
| platform | A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. |
| liquid chromatography mass spectrometry platform | A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. |
| microarray platform | A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. |
| ratio of collected to emitted light | A ratio of collected to emitted light is a datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role |
| software optimization | Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. |
| notified body role | Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive |
| allotransplantation | is the transplantation of organs between members of the same species. |
| gamma counter | A processed material which measures gamma radiation |
| trial monitor role | Trial monitor is a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study |
| positive reference substance role | Reference substance is a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response |
| polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether | triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties |
| investigation | a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). |
| evaluant role | a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role |
| reporting party role | Reporting party role is a study personnel role played by a party who reports the outcome of a study component |
| assay | A planned process with the objective to produce information about some evaluant |
| quantitative confidence value | A quantitative confidence value is a information content entity which is used to indicate the degree of uncertainty about a measurement. |
| sample preparation for assay | A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. |
| diagnosis textual entity | diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. |
| unplanned occurrence effecting an investigation | a process which is external in origin to the investigation that has an impact on the outcome. |
| eMedical record | An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. |
| culture medium role | A culture medium role is a role that inheres in a material entity and is realized in the use of that material entity by an organism grown in vitro to provide all needed nourishment. |
| electronic case report tabulation | An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. |
| polystyrene tube | a polystyrene tube is a test tube made of polystyrene |
| reagent role | Reagent role is a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances |
| role of regulator of chemical manufacturer | A regulator of chemical manufacture is a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture |
| detector reagent role | detector reagent role is a reagent role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. |
| role of certified IRB professional | is a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA |
| patient role | Patient is a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider |
| material processing | A planned process which results in physical changes in a specified input material |
| protocol testing objective | Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. |
| study subject role | study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about. |
| role of being first subject treated | First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study |
| measured expression level | A measured expression level is a datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. |
| responsible party role | A responsible party role is a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study |
| principal investigator role | Principal investigator is a responsible party role played by a person responsible for the overall conduct of a study |
| transplantation | a protocol application to replace an organ or tissue of an organism |
| biological vector role | a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. |
| pH indicator dye role | the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity |
| specimen role | a role borne by a material entity that is gained during a specimen creation process and that is realized by use of the specimen in an investigation |
| sequence feature identification objective | Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. |
| intervention design | an intervention design is a study design in which treatments (perturbations or intervention) defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. |
| worker role | Worker is a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline |
| Bernoulli trial | is an assay where the output data is a datum with one of two values denoted success and failure. |
| gene list | A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. |
| number of particles in subset | A number of particles in subset is a datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role |
| number of lost events electronic | A number of lost events electronic is a datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. |
| calibration substance role | A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance |
| molecular feature identification objective | Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. |
| hardware testing objective | Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. |
| incubator | An incubator is an instrument in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled |
| label role | Label role is a reagent role where the bearer is a material entity and which is realized in a detection of label assay |
| baseline participant role | baseline participant role is a reference participant role which is realized by making the reference to qualities at the start of the study or intervention |
| role of independent data monitoring committee | Independent data monitoring committee is a trial monitor role charged recommending whether to continue, modify, or end the trial |
| pathologist role | Pathologist is a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline |
| supernatant collection system harvesting frame | The Supernatant Collection system is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. |
| filter paper | Fliter paper is a device manufacture with the intent to provide a porous unsized paper used for filtering. |
| cell co-culturing | A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. |
| role of Institutional Review Board | the role of a organization that is realized by members reviewing study designs for their agreement with regulations |
| eSource document | an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures |
| crossover population role | crossover population role is a role realized when a participant serves as reference to itself |
| complete nutrient role | A nutrient role is a role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. |
| radiolabel role | Radiolabelrole is a label role which uses radiological decay as the signal |
| cDNA library | Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.nnALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. |
| electronic case report form | An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. |
| placebo role | Reference substance is a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response and which is physically similar in appearance to the test substance |
| autotransplantation | is the transplantation of tissue from one part of nthe body to another in the same individual. ) |
| parameter threshold | A parameter threshold is a datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role |
| study group role | study group role is a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol |
| p-value | A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. |
| population | a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area |
| nuclear magnetic resonance assay | A nuclear magnetic resonance assay is an assay used to identify the chemical structure of a compound or biological macromolecule. definition_source: www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html |
| imaging assay | An imaging assay is an assay to produce a picture of an entity. definition_source: OBI. |
| protocol optimization | Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. |
| role of pathology review board | Pathology review board is a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation |
| microtiter plate | A microtiter_plate is a flat plate with multiple wells used as small test tubes. |
| role of impartial witness | Is a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial |
| biological replicate role | biological replicate role is a reference participant role realized by equivalent treatment of participants |
| radioactivity detection | An assay in which a material's radioactivity is measured. |
| investigation agent role | Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing. |
| nutrient role | A nutrient role is a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. |
| dropout role | Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. |
| health care provider role | Healthcare provider is a worker role of providing medical care either within or outside the study timeline |
| methodology testing objective | Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. |
| analytical cytology data file | A digital entity intended to capture data in analytical cytology domain. |
| proxy respondent role | Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel |
| fluorescence compensation matrix | A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. |
| negative reference substance role | Reference substance is a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response |
| role of legally acceptable representative | is a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. |
| investigation results report | An investigation report is a report on the results of an investigation. |
| cellular feature identification objective | Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. |
| reference subject role | a study subject role in which the characteristics or responses of the participant playing the reference participant role are used for comparison or reference. |
| vital dye role | The role of a dye that is realized when used in an experiment to stain live cells |
| blinded medication role | Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance |
| sub-investigator role | Sub-investigator is a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline |
| data encoding | is a process to encode an information entity into a digital document |
| enzymatic cleavage | enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme |
| hardware optimization | Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. |
| trial statistician role | Trial statistician is a worker who analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. |
| standard error | Standard error is a quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. |
| antigen role | Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response |
| software testing objective | Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. |
| sponsor role | Sponsor is a responsible party role involved with any of the following activities: initiating, managing and funding a study |
| organization | An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. |
| feed role | Feed role is a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. |
| technical replicate role | technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay |
| dye role | Label role is a reagent role where the bearer is a material entity and which is realized in the process of dyeing or imparting color to a target material |
| cluster | A data cluster is a data set which is a subset of data that are a similar to each other in some way. |
| cohort role | a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. |
| artificially induced nucleic acid hybridization | Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. |
| DNA extraction | A DNA extraction is a nucleic acid extraction where the desired output material is DNA. |
| plan | A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. |
| sample population | A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. |
| organism feature identification objective | Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. |
| number of lost events computer | A number of lost events is a datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role |
| protocol | a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. |
| role of regulator of consumables and medical devices | A regulator of consumables and medical devices is a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices |
| adding a material entity into a target | is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. |
| analyte role | Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role |
| disease stage | a part of an occurrence of a disease process which is associated with position in the normal progression of the disease |
| intraperitoneal injection | is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe |
| precipitate | a precipitate is a material entity which is output of a precipitation process |
| protein-protein interaction detection | An assay with the objective to determine interactions between proteins, such as protein-protein binding. |
| transcription factor binding site identification | a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors |
| enrollment | enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules |
| adverse event trigger | revisit? |
| eluate | a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase |
| material to be added role | material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process |
| peritoneum | is the serous membrane that forms the lining of the abdominal cavity |
| interpreting data | the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions |
| planning | a process of creating or modifying a plan. |
| documenting | a planned process of capturing information in an enduring form with the intent to communicate this information |
| histological sample preparation | histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay |
| inductive reasoning | It is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. |
| mass analyzer | A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. |
| hypothesis driven investigation | is an investigation with the goal to test one or more hypothesis |
| hypothesis generating investigation | is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis |
| ion source | An ion source is a device that is part of a massnspectrometer that ionizes the material under analysis. The ions arenthen transported by magnetic or electric fields to the mass analyzer.nTechniques for ionization have been key to determining what types ofnsamples can be analyzed by mass spectrometry. Electron ionization andnchemical ionization are used for gases and vapors. In chemicalnionization sources, the material is ionized by chemical ion-moleculenreactions during collisions in the source. Two techniques often usednwith liquid and solid biological samples include electrospraynionization (due to John Fenn PMID 2675315.) and matrix-assisted laserndesorption/ionization (MALDI, due to M. Karas and F. Hillenkampn(Measuring Mass: From Positive Rays to Proteins by Michael A. Graysonn(Editor) (ISBN 0-941901-31-9))). |
| ion detector | An ion detector is a device that measures and recordsnthe charge induced or current produced when an ion passes by or hits ansurface. In a scanning instrument the signal produced in the detectornduring the course of the scan versus where the instrument is in thenscan (at what m/Q) will produce a mass spectrum, a record of ions as anfunction of m/Q. |
| metabolite profiling | metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism |
| light emission function | A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. |
| record function | A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation |
| magnify function | A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. |
| contain function | A contain function is a function to bound or constrain some quantity of material in some space |
| heat function | A heat function is a function that increases the internal kinetic energy of a material |
| separation function | A separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. |
| ionize process | The physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. |
| excitation function | A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. |
| freeze function | A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. |
| synthesizing function | A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. |
| perturbe function | A perturbe function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. |
| filter function | A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through |
| mechanical function | A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force. |
| gas filter function | A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture |
| liquid filter function | A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture |
| transfer function | A transfer function is a function to displace a material from one location to another. |
| electricity supply function | An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity. |
| ionization function | An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. |
| cool function | A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. |
| connection function | A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. |
| isoelectric focusing device | An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. |
| thermostatic circulator | A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid |
| energy supply function | An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy |
| information processor function | An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. |
| signal conversion function | A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. |
| blot module | A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised |
| signal amplification function | A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. |
| image acquisition function | An image acquisition function is a function to acquire an image of a material |
| image acquisition device | An image acquisition device is a device which captures a digitized image of an object |
| immobilize function | An immobilize function is a contain function to fix an entity in a defined position and prevent its movement |
| display function | A display function is a function to present information by translating that information through some lookup process into visual form. |
| environment control function | An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. |
| sort function | A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. |
| gel dryer | A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels |
| primer role | primer role is a reagent role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. |
| PCR product | is double stranded DNA that is the specified output of a polymerase chain reaction |
| viral RNA extraction | The extraction of RNA from an input material that specifically isolates viral RNA |
| nucleic acid template role | nucleic acid template role is a reference role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. |
| recombinant plasmid | A recombinant plasmid is a plasmid in which extraneous DNA has been inserted. |
| cloning vector role | A cloning vector role is a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. |
| cell cycle synchronization | cell cycle synchronization is a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle |
| polymerase chain reaction | PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. |
| cloning insert role | cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. |
| measuring glucose concentration in blood serum | An assay that determines the concentration of glucose molecules in a blood serum sample |
| reverse transcriptase | enzyme and has_function some GO:0003964 (RNA-directed DNA polymerasenactivity) |
| trypsinized material | A material entity that has undergone a process of digestion with trypsin |
| syringe | a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw |
| extract | an extract is a material entity which results from an extraction process |
| transcription profiling | trancription profiling is a process which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot |
| averaging objective | An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. |
| injection | injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. |
| enzyme | (protein or rna) or has_part (protein or rna) andnhas_function some GO:0003824 (catalytic activity) |
| intraperitoneal administration | The administration of a substance into the peritoneum of an organism |
| plasmid | plasmid = DNA and has_quality circular and has_functionn(is_realized_as some gene expression) GO:0010467 |
| injection into organ section | A process in which an input substance is injected into a organ section. |
| polyacrylamide gel | agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution |
| DNA sequence feature detection | An assay with the objective to determine a sequence feature of DNA |
| adding material objective | is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity |
| genotyping | a process which generates data about a genotype from a specimen of genomic DNA. A variety ofntechniques and instruments can be used to produce information about sequence variation at particular genomic positions. |
| needle | a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. |
| analyte measurement objective | is an assay objective to determine the presence or concentration of an analyte in the evaluant |
| DNA sequence variation detection | DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule. |
| agarose gel | agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution |
| assay objective | is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role) |
| heart | The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions |
| analyte assay | An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. |
| target of material addition role | target of material addition role is a role realized by an entity into which a material is added in a material addition process |
| mass measurement assay | a process to determine the mass of an evaluant |
| identification | a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval |
| intra cellular electrophysiology recording | An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular |
| packed column | A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. |
| regulatory agency | A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. |
| normalized data set | A normalized data set is a data set that is produced as the output of a normalization data transformation. |
| measure function | Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. |
| extracellular electrophysiology recording | An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data |
| consume data function | Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. |
| material transformation objective | is the objective to create an specific output object from input materials. |
| manufacturing | Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process |
| manufacturing objective | is the objective to manufacture a material of a certain function (device) |
| column chromatography detector | There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. |
| Bruker autosampler | A Bruker autosampler is an autosampler made by Bruker. |
| organic acid column | An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. |
| thermal conductivity detector | The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). |
| Bruker US 2 NMR magnet | An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. |
| protein column | A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. |
| solvent mixer | A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. |
| mass spectrometry assay | This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically. |
| study design execution | a planned process that realizes the concretization of a study design |
| Bruker NMR Case sample changer | The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. |
| nano pump system | A pump system optimized for nano flow chromatography. |
| Bruker AutoClean system | NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. |
| manual injection system | The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. |
| Varian GEMINI spectrometer | An older Varian Broadband NMR spectrometer. |
| column connector | A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. |
| solid NMR probe | An NMR probe that is designed to hold a solid sample. |
| Bruker high resolution probe | BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.n defprov: Bruker website |
| chromatography detector | A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. |
| normal phase column | A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. |
| APOLLO console | The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. |
| NMR sample holder | An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. |
| chromatography instrument | Any instrument that is used to carry out a chromatography experiment. |
| continuous wave NMR instrument | Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). |
| fourier transformation NMR instrument | In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. |
| nitrogen phosphorous detector | The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. |
| cation exchange column | A cation exchange column is a chromatography column that is used in cation exchange chromatography. |
| direct detection NMR probe | An NMR probe designed to allow the direct detection of acquisition nuclei. |
| Bruker B-ACS system | The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. |
| rapid resolution column | A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. |
| liquid chromatography autosampler | Designed to perform capillary LC with injection of sample volumes ranging from nL to L. |
| vacuum degasser | A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. |
| capillary column | A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. |
| sample inlet | The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. |
| NMR tube washing system | An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. |
| NMR console | A component of an NMR instrument that controls the activities of the other components. |
| dual loop autosampler | A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). |
| variable wavelength detector | A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. |
| Bruker LC-NMR platform | The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. |
| sample injection system | An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. |
| multiple wavelength detector | A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. |
| photoionization detector | The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. |
| gas generator | An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. |
| column jacket | A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. |
| electron capture detector | The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. |
| reversed phase column | A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. |
| injector lubricant | A lubricant used in liquid chromatography that eases sample injector penetration. |
| isolation of cell population | is a process in which a population of cells with certain characteristics is isolated from a larger population |
| DISCOVERY console | The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing networkn defprov: tecmag website |
| Bruker AMX series NMR instrument | A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. |
| chromatofocusing column | A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. |
| NMR probe | Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. |
| NMR magnet | A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. |
| trap column | A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. |
| flow probe | An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. |
| clinical chemistry assay | clinical chemistry assay is a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism. |
| flame ionization detector | A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. |
| vial | A vial is a cylindrical container often made from glass tubing. |
| magic angle spinning rotor | A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. |
| Varian VXR spectrometer | A Varian NMR spectrometer. |
| splitless GC injector | Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. |
| preparative autosampler | For preparative LC with injection of sample volumes ranging from L to mL ranges. |
| flow high resolution probe | Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. |
| Liquid chromatography valve | A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. |
| JEOL NMR probe | An NMR probe that is manufactured by JEOL. |
| Bruker UltraShield Plus NMR magnet | An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. |
| Bruker CryoProbe | The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. |
| column cartridge | A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. |
| affinity column | An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. |
| tecmag NMR instrument | An NMR instrument that is manufactured by tecmag. |
| gel filtration column | A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. |
| fraction collector | A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. |
| copy number variation profiling | copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping. |
| in-line filter | A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. |
| imaging NMR probe | An NMR probe that is designed for generating pictures from sample states via NMR imaging. |
| isolation of adherent cells | is a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. |
| Bruker AC series NMR instrument | A series of older Bruker NMR magnets, now out of production. |
| gas chromatography equipment | Any device used in a gas chromatography experiment. |
| syringe filter | A small membrane filter of defined pore size, that filters samples from a syringe. |
| Bruker SampleRail system | This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system.n The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. |
| column compartment | For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. |
| capillary pump system | A pump system optimized for capillary chromatography. |
| evaporative light scattering detector | The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. |
| isolation of PBMCs | is a process in which cells with a single nucleus are isolated from a blood sample |
| column cartridger | A chromatography device where the column cartridge is inserted into and stabilised. |
| nitrogen generator | A gas generator that generates nitrogen gas. |
| needle assembly | The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet |
| reverse transcribed polymerase chain reaction | reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. rt-pcr is applied to test the presence and possibly the abundance of a transcript in the entity of organismal origin |
| Bruker Capillary LC-NMR platform | Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. |
| gas chromatography oven | A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. |
| autosampler | An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. |
| isocratic pump system | A pump system optimized for isocratic chromatography. |
| flash pump system | Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). |
| Varian UNITY INOVA spectrometer | The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. |
| liquid NMR probe | An NMR probe that is designed to hold a liquid sample. |
| ion exchange column | An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. |
| Bruker NMR probe | An NMR probe that is manufactured by Bruker. |
| anion trap column | An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. |
| fluorescene detector | A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. |
| tecmag EAGLE probe | The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. |
| electrical conductivity detector | The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. |
| NMR instrument | An Instrument which is used to carry out a NMR analysis of some sample. |
| Bruker UltraShield NMR magnet | An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. |
| piston-seal | The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. |
| mass selective detector | A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. |
| spin column | A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. |
| manufacturer role | Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. |
| transfer line | A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. |
| gradient pump system | A pump system optimized for gradient chromatography. |
| high temperature column | A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. |
| Bruker Ultrastabilized NMR magnet | An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. |
| scattered molecular aggregate | A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates |
| molecular concentration | A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. |
| NMR sample tube | The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. |
| Varian UNITY spectrometer | The predecessor series of the Varian UNITY INOVA spectrometer. |
| AVANCE II spectrometer | A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. |
| y-column connector | A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. |
| Bruker LC-NMR/MS platform | Includes the connection to a high-resolution TOF-LC-MS system. |
| refractive index detector | For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. |
| anion exchange column | An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. |
| plunger column | A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. |
| flame photometric detector | The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. |
| chromatography pump system | Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). |
| Bruker 1mm MicroProbe | Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling availablen defprov: Bruker website |
| Bruker BEST NMR system | The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. |
| chromatography detector filter | An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. |
| cation trap column | A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. |
| column adapter | An Adapter that enabled the connection of a column to additional devices. |
| pulsed amperometric detector | A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). |
| Bruker NMR instrument | An NMR instrument that is manufactured by Bruker. |
| Bruker NMR magnet | An NMR magnet that is manufactured by Bruker. |
| ozone-induced chemiluminescence detector | Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. |
| tecmag NMR console | An NMR console manufactured by tecmac. |
| JEOL NMR instrument | An NMR instrument that is manufactured by JEOL. |
| chromatography consumable | A chromatography consumable is a consumable that is used in a chromatography experiment. |
| column frit | A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). |
| liquid chromatography column | A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. |
| detector lamp | A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. |
| chart recorder | The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. |
| open tubular column | An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. |
| high resolution magic angle spin probe | Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.n defprov: Bruker websiten alt High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. |
| hydrogen generator | A gas generator that generates hydrogen gas. |
| glass column | A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. |
| auto injector | A gas chromatography device that can auto-inject a small number of samples an inlet. |
| Varian NMR instrument | An NMR instrument that is manufactured by Varian. |
| Bruker MATCH tube holder system | The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. |
| Bruker SPE-NMR platform | A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. |
| guard column | Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. |
| protein expression profiling | a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays |
| high resolution probe with automatic tuning and matching | The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. |
| fluorine-induced chemiluminescence detector | A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. |
| size exclusion column | A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. |
| chromatography splitter | An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. |
| Bruker micro imaging probe | For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. |
| custom made column | A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. |
| gel permeation column | A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. |
| NMR spectroscopy | NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. |
| Bruker SampleJet system | Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. |
| JEOL ECX NMR spectrometer | The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. |
| DNA sequencing | DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. |
| quaternary pump system | A pump system that pump and mix up to four different solvents in parallel. |
| carbon nanotube column | Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. |
| Bruker solid magic angle spinning probe | Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. |
| hematology | hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments |
| Varian MERCURY spectrometer | MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. |
| Bruker Metabolic Profiler | An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. |
| column heater | The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. |
| DNA methylation profiling | DNA methylation profiling is a process which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. |
| JEOL CapNMR probe | The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 B5l flowcell with an NMR active volume of 2.5 B5l, and a 10 B5l flowcell with an NMR active volume of 5 B5l. The fluidic connections are 75 B5m i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. |
| acquisition computer | A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. |
| gas chromatography detector | A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. |
| gas purifier | Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. |
| material separation objective | is an objective to transform a material entity into spatially separated components. |
| indirect detection probe | An NMR probe designed to allow the indirect detection of acquisition nuclei. |
| JEOL ECA NMR spectrometer | The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. |
| atomic emission detector | Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. |
| clustered data set | A clustered data set is a data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. |
| data set of features | A data set of features is a data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. |
| differential expression analysis data transformation | A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of |
| urine specimen | is a portion of urine collected from an organism |
| material combination | is a material processing with the objective to combine two or more material entities as input into a single material entity as output. |
| fuzzy clustering objective | A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. |
| device setting | Device_setting inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device |
| blood specimen | a material entity derived from a portion of blood collected from an organism |
| data set of predicted values according to fitted curve | A data set of predicted values according to fitted curvet is a data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. |
| data representational model | Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. |
| specimen creation | a planned process with the objective of obtaining specimen. |
| background corrected data set | A background corrected data set is a data set that is produced as the output of a background correction data transformation. |
| ELISA | ELISA is an assay where an enzyme linked antibody is used to detect a plate bound material in a liquid (the evaluant) utilizing a chemiluminescent reaction. The detected signal is proxy for the concentration of an analyte in the evaluant. |
| error corrected data set | An error corrected data set is a data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). |
| class prediction data transformation | A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. |
| BrdU incorporation assay | A BrdU incorporation assay is an assay to detect actively replicating cells. BrdU is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA. |
| intracellular cytokine staining assay | The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. |
| background correction data transformation | A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. |
| MHC multimer assay | An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer |
| error correction data transformation | An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. |
| tritiated thymidine incorporation assay | A tritiated thymidine incorporation assay is an assay to detect actively replicating cells. Tritiated thymidine is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine can then be detected thus indicating cells that were actively replicating their DNA. |
| sample from organism | a sample from organism is a material obtained from an organism in order to be a representative of the whole |
| statistical hypothesis test | A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. |
| center value | A centre value is a data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. |
| statistical hypothesis test objective | is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation |
| reduced dimension data set | A reduced dimension data set is a data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. |
| portioning objective | is the objective to separate material into multiple portions, each of which contains a similar composition of the input material. |
| average value | An average value is a data item that is produced as the output of an averaging data transformation and represents the average value of the input data. |
| whole organism preparation | A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained |
| separation into different composition objective | is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities) |
| study result | Study result is an information content entity that is a specified data output of a study. |
| specimen creation objective | A specimen creation objective is to obtain and store a material entity for potential use as an input during an investigation |
| creating a mixture of molecules in solution | is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. |
| material combination objective | is an objective to obtain an output material that contains several input materials. |
| nucleotide overhang cloning | Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation |
| rodent care protocol | A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. |
| 454 Genome Sequence 20 | is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which arencontrolled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. |
| immunoprecipitation | is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity |
| ABI 377 automated sequencer | is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. |
| recombination enzyme based cloning | a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector |
| MeDIP-SEQ assay | is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. |
| animal feeding | animal feeding is a process in which animals are provided with food |
| chain termination sequencing | is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position |
| AB SOLiD System | is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation |
| Helicos sequencing | is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. |
| DNA ligase | A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule |
| survival assessment | Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time |
| support vector machine | A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. |
| self-organizing map | A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. |
| 454 Genome Sequencer FLX | is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which arencontrolled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. |
| Illumina Genome Analyzer II | is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology |
| decision tree induction objective | A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. |
| Edman degradation | is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues. |
| SOLiD sequencing | is a DNA sequencing which allows sequence identification by relying on the following steps:n1. Primers hybridize to the P1 adapter sequence within the library template.n2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction.n3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length.n4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles |
| decision tree building data transformation | A decision tree building data transformation is a data transformation that has objective decision tree induction. |
| laboratory animal care | laboratory animal care is a process that realizes an animal care protocol that specifies how animals are kept and maintained |
| yeast artificial chromosome vector | A yeast artificial chromosome vector is a DNA molecule that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences |
| Li-Cor 4300 DNA Analysis System | is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing |
| library preparation | is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. |
| pathogen challenge | A pathogen challenge is the administration of a live pathogenic organism to a host |
| GenePattern software | Is software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. |
| graph of vertices | A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. |
| animal care protocol | An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes |
| ChIP-SEQ assay | is an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. |
| HeliScope Single Molecule Sequencer | is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry |
| pathogen role | pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role |
| vaccine preparation | vaccine preparation is a manufacturing process to produce a vaccine |
| adjuvent role | Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. |
| glucose tolerance test | is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. |
| paired-end library | is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs |
| DNA sequencing by ligation | is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step. |
| Solexa sequencing | is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. |
| host role | host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role |
| peak matching | Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold |
| k-nearest neighbors | A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. |
| rodent care | rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. |
| cloning plasmid | A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. |
| pyrosequencing | is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template.nnssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. |
| recombinant vector | A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. |
| restriction enzyme | A restriction enzyme is an enzyme that has a specific target cleavage sites within nucleic acids |
| DNA sequencing by synthesis | is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. |
| NTP-2000 | NTP-2000 is a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents |
| single fragment library | is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs |
| cloning vector | A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. |
| restriction enzyme based cloning | restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. |
| Student's t-test | Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. |
| material sample role | A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. |
| topologically preserved clustered data set | A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. |
| nucleic acid restriction enzyme digest | A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site |
| immune response assay | Is an assay with the objective to determine information about an immune response |
| material sampling process | A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity |
| material sample | A material entity that has the material sample role |
| bisulfite sequencing | is a DNA sequencing which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. |
| CART | A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. |
| independent variable specification | a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled |
| dependent variable specification | dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. |
| anticoagulant-containing test tube | A 'blue top' test tube that contains anticoagulant for storing blood specimens' |
| controlled variable specification | Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. |
| human antithrombin-III (AT-III) in blood assay | An assay to measure the amount of antithrombin III in blood. |
| fluorescently labeled MHC multimer | A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand |
| survival rate | Survival rate is a measurement data that represents the percentage of people ornanimals in a study or treatment group who are alive for a given periodnof time after diagnosis or initiation of monitoring. |
| recombinant BAC cloning | Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material |
| multiple testing correction objective | A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously |
| statistical model validation | A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. |
| double blind study execution | A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated |
| glucometer | A measurement device with the function to measure and record the level/amount of glucose in a blood sample |
| purification objective | The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest |
| primary structure of protein | The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together |
| capsule shell | a small rounded gelatinous container |
| recombinant phage cloning | Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. |
| cross linking | A process in which bonds are created that link one polymer to another |
| spike train datum | A spike train datum is a measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. |
| prothrombin time assay | The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma. |
| denaturing | Is a process in which the tertiary or secondary structure of a polymer is disrupted |
| informing investigator of subject study arm | A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. |
| antithrombin-III (AT-III) berichrome assay | An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard |
| material maintenance objective | is the objective to maintain some or all of the qualities of a material over time. |
| presentation of stimulus | a planned process in which an organism is exposed to some stimulus with the intent to invoke an action |
| spectrolyse heparin antifactor-Xa assay | A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma.nnThe principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration. |
| amplified DNA | DNA that has been produced in an enzymatic amplification process |
| informed consent process | a planned process in which subject is taught key facts about a clinical trial both before deciding whether or not to participate, and throughout the study. Agents of the investigation, such as doctors and nurses involved in the trial, explain the details of the study. |
| primary structure of DNA macromolecule | a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. |
| measuring neural activity in the caudate nucleus | The process of measuring neural activity in the caudate nucleus |
| to be treated with active ingredient role | A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient |
| guar gum | Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. |
| Berichrom(r) Antithrombin III (A) Kit | For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution |
| micro electrode | An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. |
| fucoidan | Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). |
| calibration | A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. |
| anticoagulant tube storage of blood specimen | Storage of a blood specimen in a tube with anticoagulant |
| activated partial thromboplastin time (aPTT) assay | An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms. |
| filled capsule | A pill in the form of a small rounded gelatinous container with medicine inside. |
| single blind study execution | A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated |
| thrombin time assay | A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time |
| recombinant YAC cloning | Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material |
| to be treated with placebo role | A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo |
| treatment portion of study execution | A planned process, part of a study design execution, during which the treatment of subjects is ongoing |
| pill | A dose of medicine or placebo in the form of a small pellet. |
| research organization | An organization formed with a goal to have its members conduct investigations |
| primary structure of sequence macromolecule | A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds |
| DNA residue methylation | =def a quality of a DNA residue that has a methyl group attached to it |
| measurement device | a processed material created to have the function to measure |
| manufacturer | A person or organization that has a manufacturer role |
| test tube | A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material |
| oral ingestion of pill | An adding a material entity to target with the entity is a pill and the target is the mouth |
| material maintenance | a process with that achieves the objective to maintain some or all of the characteristics of an input material over time |
| unblinding process | The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials |
| subject agrees they understand informed consent document | A process in which a subject receives an informed consent document and agrees that they have understood it |
| informing subject of study arm | A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. |
| Sysmex CA-6000 Coagulation Analyzer | The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays |
| hospital | A medical organization at which sick or injured people are given clinical care |
| primary structure of RNA molecule | The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together |
| test substance role | A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation |
| injection function | The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. |
| Epstein Barr virus transformed B cell | A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity |
| chimera | An organism which contains cells or tissues with a different genotype |
| anatomical entity | An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' |
| blood plasma | blood plasma is a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. |
| blood serum specimen | A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. |
| organism | A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. |
| immortal cell | a cell derived from a multicellular organism that has the potential to replicate indefinitely |
| fragment derived from protein | A material entity which is derived from a protein |
| phosphate buffered saline solution | Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). |
| specimen | A material entity that has the specimen role. |
| cell line cell | A material entity that represents generations of a primary culture. |
| immortalized cell line | An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an immortalization process |
| xenograft | A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. |
| cell culture | a cell culture is a material entity consisting of a population of cells that is maintained in vitro |
| primary cell culture | a primary cell culture is a cell culture where the cells derive from a fresh tissue source. |
| cell line culture | a cell line culture is a cell culture where the cells grown are from a cell line, long term culture of cells that are replicating continuously. The cell population is homogenous but not clonal |
| clonal cell culture | a clonal cell culture is a cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell. |
| screening library | a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? |
| synthetic peptide | a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment |
| organ section | A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) |
| bronchial alveolar lavage | Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. |
| polymer | A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. |
| glucose in solution | A scattered aggregate of glucose molecules in a liquid |
| data transformation | A data transformation is a process which produces output data from input data |
| logistic-log curve fitting | A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). |
| logit-log curve fitting | A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. |
| log-log curve fitting | A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. |
| feature extraction objective | A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. |
| biexponential transformation | A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. |
| box-cox transformation | A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. |
| hyperlog transformation | A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. |
| loess scale group transformation one-channel | A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. |
| logical transformation | A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. |
| loess scale group transformation two-channel | A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. |
| loess global transformation one-channel | A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. |
| split-scale transformation | A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. |
| loess global transformation two-channel | A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. |
| sine transformation | A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. |
| cosine transformation | A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. |
| loess group transformation one-channel | A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. |
| loess group transformation two-channel | A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. |
| homogeneous polynomial transformation | A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. |
| linlog transformation | A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. |
| variance stabilizing transformation | A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. |
| loess global transformation | A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. |
| loess group transformation | A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. |
| loess scale group transformation | A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. |
| total intensity transformation single | A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. |
| total intensity transformation paired | A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). |
| quantile transformation | A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. |
| mean centering | A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. |
| median centering | A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. |
| differential expression analysis objective | A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. |
| K-fold cross validation method | is a data transformation which randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used . Objective: cross-validation |
| leave one out cross validation method | is a data transformation which involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data. Objective: cross-validation |
| jackknifing method | Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method |
| boostrapping | Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient |
| Benjamini and Hochberg false discovery rate correction method | A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate |
| pareto scaling | A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. |
| modular decomposition | Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. |
| k-means clustering | A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). |
| hierarchical clustering | A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). |
| average linkage hierarchical clustering | An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster. |
| complete linkage hierarchical clustering | A complete linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. |
| single linkage hierarchical clustering | A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster. |
| Benjamini and Yekutieli false discovery rate correction method | A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate |
| dimensionality reduction | A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. |
| principal components analysis dimensionality reduction | A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. |
| probabilistic algorithm | A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. |
| expectation maximization | EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. |
| global modularity calculation | A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. |
| dye swap merge | A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. |
| moving average | A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. |
| replicate analysis | A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. |
| b cell epitope prediction | A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. |
| mhc binding prediction | An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. |
| t cell epitope prediction | A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. |
| data imputation | Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. |
| continuum mass spectrum | A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. |
| characteristic path length calculation | Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices |
| centroid mass spectrum | A centroid mass spectrum is a data transformation that is generated by drawing a line from the tip of each peak to the base of the graph. Centroid mass spectra contain discrete peaks of zero width. |
| Holm false discovery rate correction method | is a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level N1 in the strong sense. Objective: multiple testing correction |
| edge weighting | Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. |
| loess transformation | A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. |
| curve fitting data transformation | A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. |
| family wise error rate correction method | A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. |
| submatrix extraction | A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) |
| row submatrix extraction | A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. |
| column submatrix extraction | A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. |
| gating | Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. |
| descriptive statistical calculation objective | A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. |
| mean calculation | A mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. |
| network analysis | A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. |
| sequence analysis objective | A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. |
| longitudinal data analysis | Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. |
| survival analysis objective | A data transformation objective which has the data transformation aims to model time to event data; the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables |
| mass spectrometry analysis | A data transformation which has the objective of spectrum analysis. |
| spread calculation data transformation | A spread calculation is a data transformation that has objective spread calculation. |
| Kaplan Meier | a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) |
| multiple testing correction method | A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate |
| determining inter-rater agreement | a planned process with objective of determining the concordance or agreement between human judges. |
| Westfall and Young family wise error rate correction | Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing |
| polynomial transformation | A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. |
| logarithmic transformation | A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. |
| exponential transformation | An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. |
| non-negative matrix factorization | Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. |
| soft independent modeling of class analogy analysis | Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. |
| discriminant function analysis | Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. |
| canonical variate analysis | canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. |
| linear discriminant functional analysis | Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. |
| regression analysis method | Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. |
| multiple linear regression analysis | multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written asn Y = beta_0 + beta_1 X_1 + beta_2 X_2 + cdots +beta_p X_p + varepsilonnwhere beta_0 = 0 is the intercept ("constant" term), the beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. |
| principal component regression | The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. |
| partial least square regression analysis | Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so thatnY = b0 + b1X1 + b2X2 + ... + bpXpnIn this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. |
| discriminant analysis | Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. |
| partial least square discriminant analysis | PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. |
| eh transformation | An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. |
| b transformation | A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. |
| s transformation | An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. |
| data visualization | An planned process that creates images, diagrams or animations from the input data. |
| similarity calculation | A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. |
| euclidean distance calculation | An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. |
| pearson correlation coefficient calculation | A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. |
| loess fitting | A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). |
| mode calculation | A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. |
| quantile calculation | A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. |
| median calculation | A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. |
| variance calculation | A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. |
| standard deviation calculation | A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. |
| interquartile-range calculation | The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. |
| skewness calculation | A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment |
| kurtosis calculation | A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html |
| data combination | A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. |
| network graph construction | A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. |
| weighted network graph construction | A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. |
| directed network graph construction | A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. |
| node quality calculation | A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. |
| node degree calculation | A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. |
| quantitative node degree calculation | A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. |
| node in-degree calculation | A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. |
| node out-degree calculation | A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. |
| node shortest path identification | A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. |
| edge quality calculation | A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. |
| edge betweenness calculation | An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. |
| network subgraph quality calculation | A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. |
| subgraph degree calculation | A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. |
| quantitative subgraph degree calculation | A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. |
| mathematical feature | feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation |
| log base | The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. |
| subgraph in-degree calculation | A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. |
| subgraph out-degree calculation | A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. |
| intra subgraph connectivity calculation | A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. |
| subgraph modularity calculation | A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. |
| network graph quality calculation | A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. |
| unit-variance scaling | A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. |
| MA transformation | An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. |
| exponential base | The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). |
| polynomial degree | The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. |
| number of variables | The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. |
| agglomerative hierarchical clustering | An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining. |
| divisive hierarchical clustering | A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. |
| data partitioning | Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. |
| data vector reduction objective | Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. |
| generalized family wise error rate correction method | A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. |
| quantile number of false positives correction method | A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' |
| tail probability for the proportion of false positives correction method | A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. |
| false discovery rate correction method | A false discovery rate correction method is a multiple testing procedure that controls for the expected value of the proportion of false positives among the rejected hypotheses. |
| proportion of expected false positives correction method | A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. |
| quantile proportion of false positives correction method | A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). |
| data transformation objective | A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. |
| data normalization objective | A normalization objective is a data transformation objective where the aim is to removensystematic sources of variation to put the data on equal footing in ordernto create a common base for comparisons. |
| correction objective | A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself |
| normalization data transformation | A normalization data transformation is a data transformation that has objective normalization. |
| averaging data transformation | An averaging data transformation is a data transformation that has objective averaging. |
| partitioning data transformation | A partitioning data transformation is a data transformation that has objective partitioning. |
| partitioning objective | A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. |
| background correction objective | A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. |
| curve fitting objective | A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. |
| class discovery data transformation | A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. |
| Fisher's exact test | Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two categorical variables. |
| center calculation objective | A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. |
| class discovery objective | A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. |
| class prediction objective | A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) andnclass labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. |
| spread calculation objective | is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set |
| center calculation data transformation | A center calculation data transformation is a data transformation that has objective of center calculation. |
| data vector reduction data transformation | A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. |
| scaling objective | is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum |
| descriptive statistical calculation data transformation | A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. |
| scaling data transformation | A scaling data transformation is a data transformation that has objective scaling. |
| error correction objective | An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. |
| sequence analysis data transformation | A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. |
| cross validation objective | A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. |
| merging objective | A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. |
| clustered data visualization | A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. |
| gene list visualization | Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. |
| classified data visualization | A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. |
| background corrected data visualization | A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. |
| survival analysis data transformation | A data transformation which |
| proportional hazards model estimation | Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. |
| correlation study objective | A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, O) which indicates the strength and direction of a relationship between two random variables. |
| spectrum analysis objective | is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. |
| tandem mass spectrometry | Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). |
| gas chromatography mass spectrometry | Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and ngas chromatography for the qualitative as well as quantitative ndeterminations of compounds. |
| chi square test | The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. |
| sequential design | Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does |
| observation design | observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. |
| collection (of entities of organismal origin) | a collection is a bfo:aggregate object, that is a set of material object of the same kind |
| pool of specimens | A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. |
| chemical solution | A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. |
| buffer role | is a role which inheres in some molecular entity realized during the process of buffering |
| solvent role | solvent role is a role played by a chemical entity capable of ensuring the dissolution of another chemical entity, thereby exhibiting solvatation properties |
| solute role | solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution |
| comet assay | a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions. |
| PCR-SSCP assay | a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure. |
| liver | liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates |
| adipose tissue | adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. |
| denatured polymer | Is a polymer which has lost secondary or tertiary structure |
| decapitated organism | decapitated organism is an organism which has had it's head removed |
| validated information | validated is a conferred qualify which inheres in material resulting from an validation process |
| curated | A information content entity that has been created by a curator |
| randomized group participant role | is a role borne by an organism and realized by some group randomization process |
| methylated polymer | A methylated polymer which has artificially acquired one or more methyl groups |
| genetically modified organism | Is a organism that is the output of a genetic transformation process |
| predicted | predicted is a |
| mean-centered data | is a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value |
| edited information | A document that has gone through a process of review and modifications |
| dissolved material entity | A material entity that has been going through a process of being put into solution |
| extraction | A material separation in which a desired component of an input material is separated from the remainder |
| filtration | filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device |
| centrifugation | centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation |
| staining | Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. |
| washing | washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. |
| irradiation | irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves |
| polymerization | polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight |
| trypsination | trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity |
| enzymatic ligation | An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity |
| storage | storage is a process by which material entities are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability |
| cell lysis | cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. |
| electrocution | electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. |
| cervical dislocation | cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion |
| asphyxiation | asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms. |
| intentional overdosing | intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death |
| decapitation | decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..) |
| group randomization | A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. |
| activation | activation is a process by which a material entity status is modified and conferred a capability of reactingn(this sounds like a circular definition , hugh!) |
| immobilization | immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. |
| nucleic acid hybridization | a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. |
| elution | the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions) |
| DNA Subtraction | DNA subtraction is a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. |
| document editing | editing is a process which checks for and corrects errors in spelling, punctuation, capitalization, grammar, and usage; |
| prediction | a process by which an event or an entity is described before it actually happens or is being discovered and identified. |
| validation | a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results |
| electroporation | Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA |
| digital curation | Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. |
| A10-Analyzer | A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. |
| A40-MiniFCM | A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. |
| analog-to-digital converter | An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. |
| flow cytometer analyzer | An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. |
| arc lamp | Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. |
| argon ion laser | An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. |
| avalanche photodiode | An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. |
| Bactiflow | A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. |
| band pass filter | A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. |
| BioSorter1000 | A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. |
| BioSorter2000 | A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. |
| BioSorter250 | A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. |
| BioSorter500 | A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. |
| Cell Lab Quanta SC | A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. |
| charge plate | Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. |
| cell sorter collection tube | Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. |
| Cyan | A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. |
| CYFlow ML | A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. |
| CyFlow SL | A CyFlow_Sl is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. |
| CyFlow SL3 | A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. |
| CyFlow Space | A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. |
| CytoBuoy | A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. |
| CytoSence | A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. |
| CytoSub | A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. |
| dichroic filter | A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. |
| dichroic mirror | A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. |
| differential pressure gauge | Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. |
| diode laser | A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. |
| dye laser | A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. |
| FACS Calibur | The FACS Calibur is one of the most popular cytometers in use for research. |
| FACS Canto | A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. |
| FACS Canto2 | A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. |
| FACS Scan | A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. |
| FACSAria | A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. |
| FACSvantage | The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. |
| FC 500 | A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. |
| flow cell | Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. |
| flow cytometer | A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. |
| fluid pressure regulator | Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. |
| gas laser | A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. |
| Guava EasyCyte Mini | A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. |
| Guava EasyCyte Plus | A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. |
| Guava Personal Cell Analysis | A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. |
| Guava Personal Cell Analysis-96 | The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. |
| helium cadmium ion laser | A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. |
| helium neon ion laser | A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. |
| Amnis ImageStream | The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow.nIt has both components, an Image cytometer and a flow cytometer. |
| inFlux Analyzer | The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. |
| Influx Cell Sorter | A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. |
| interrogation_point | Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. |
| ion laser | An ion laser is a gas laser which uses an ionized gas as its lasing medium. |
| jet_in_air_flow_chamber | A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. |
| krypton ion laser | A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. |
| LactoScope C4 | A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. |
| laser | A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. |
| light source | A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. |
| logarithmic voltage amplifier | A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. |
| long pass filter | A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. |
| LSR2 | A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. |
| Luminex 100 | The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. |
| Luminex 200 | A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation |
| MACS Quant | A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. |
| metal vapor laser | A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. |
| mixed argon-krypton gas laser | A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. |
| MoFlo | A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. |
| multi-well plate | A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. |
| neodymium-YAG laser | A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. |
| obscuration bar | An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. |
| optical filter | An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. |
| optical subsystem | An optical subsystem is an instrument or part of an instrument that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. |
| particle delivery vessel | Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. |
| photodetector | A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. |
| photodiode | A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. |
| photomultiplier tube | A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. |
| piezo electric crystal | Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell. |
| plate loader | Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. |
| preamplifier | A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. |
| quartz cuvette flow chamber | A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. |
| Reflection | A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. |
| cytometer sample tube | A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. |
| sheath tank | Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. |
| short pass filter | A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. |
| solid state laser | A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. |
| Somacount | A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. |
| SomaScope | The SomaScope is an instrument to quantify somatic cells in milk. |
| flow cytometer sorter | A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. |
| syringe pump | Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. |
| voltage amplifier | A voltage amplifier is a device that amplifies the voltage signal. |
| waste tank | Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. |
| DNA sequencer | A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. |
| array scanner | An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip |
| arrayer | An arrayer is an instrument which deposits biological material onto a substrate in a defined pattern. |
| centrifuge | A centrifuge is an instrument, generally driven by a motor, that puts an object in rotation around a fixed axis, applying force perpendicular to the axis. The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density. |
| computer | A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. |
| heating block | A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay |
| homogenizer | A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. |
| hybridization chamber | A container which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. |
| hybridization station | An instrument which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. |
| liquid handler | A liquid_handler is an instrument used for automated liquid transfer and handling. |
| oligonucleotide synthesizer | An instrument used to chemically synthesize oligonucleotides. |
| sonicator | An instrument that converts a variable electrical current to mechanical vibration of a metallic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions. |
| spectrophotometer | A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. |
| thermal cycler | An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. |
| vacuum dryer | An instrument which removes liquid by the application of negative pressure, i.e. vacuum. |
| vortexer | A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. |
| microarray wash station | A microarray wash station is an instrument used to wash Affymetrix-type arrays. |
| temperature control bath | A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. |
| molecular crosslinker | A molecular crosslinker is an instrument that is able to chemically join two or more molecules. |
| image cytometer | An image_cytometer is an instrument for image-based study or measurement of cells. |
| cytometer | A cytometer is an instrument for counting and measuring cells. |
| gel tank | A gel tank is a device which holds a gel and running buffers to allow electrophoresis |